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Zhang W, Chen K, Tian W, Zhang Q, Sun L, Wang Y, Liu M, Zhang Q. A Novel and Robust Prognostic Model for Hepatocellular Carcinoma Based on Enhancer RNAs-Regulated Genes. Front Oncol 2022; 12:849242. [PMID: 35646665 PMCID: PMC9133429 DOI: 10.3389/fonc.2022.849242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 04/01/2022] [Indexed: 11/13/2022] Open
Abstract
Evidence has demonstrated that enhancer RNAs (eRNAs) play a vital role in the progression and prognosis of cancers, but few studies have focused on the prognostic ability of eRNA-regulated genes (eRGs) for hepatocellular carcinoma (HCC). Using gene expression profiles of HCC patients from the TCGA-LIHC and eRNA expression profiles from the enhancer RNA in cancers (eRic) data portal, we developed a novel and robust prognostic signature composed of 10 eRGs based on Lasso-penalized Cox regression analysis. According to the signature, HCC patients were stratified into high- and low-risk groups, which have been shown to have significant differences in tumor immune microenvironment, immune checkpoints, HLA-related genes, DNA damage repair-related genes, Gene-set variation analysis (GSVA), and the lower half-maximal inhibitory concentration (IC50) of Sorafenib. The prognostic nomogram combining the signature, age, and TNM stage had good predictive ability in the training set (TCGA-LIHC) with the concordance index (C-index) of 0.73 and the AUCs for 1-, 3-, and 5-year OS of 0.82, 0.77, 0.74, respectively. In external validation set (GSE14520), the nomogram also performed well with the C-index of 0.71 and the AUCs for 1-, 3-, and 5-year OS of 0.74, 0.77, 0.74, respectively. In addition, an important eRG (AKR1C3) was validated using two HCC cell lines (Huh7 and MHCC-LM3) in vitro, and the results demonstrated the overexpression of AKR1C3 is related to cell proliferation, migration, and invasion in HCC. Altogether, our eRGs signature and nomogram can predict prognosis accurately and conveniently, facilitate individualized treatment, and improve prognosis for HCC patients.
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Affiliation(s)
- Wei Zhang
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Kegong Chen
- Department of Cardio-Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Department of Ultrasound, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wei Tian
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Qi Zhang
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Lin Sun
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Yupeng Wang
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Meina Liu
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Qiuju Zhang
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
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2
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Rekvig OP. The Anti-DNA Antibodies: Their Specificities for Unique DNA Structures and Their Unresolved Clinical Impact-A System Criticism and a Hypothesis. Front Immunol 2022; 12:808008. [PMID: 35087528 PMCID: PMC8786728 DOI: 10.3389/fimmu.2021.808008] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is diagnosed and classified by criteria, or by experience, intuition and traditions, and not by scientifically well-defined etiology(ies) or pathogenicity(ies). One central criterion and diagnostic factor is founded on theoretical and analytical approaches based on our imperfect definition of the term “The anti-dsDNA antibody”. “The anti-dsDNA antibody” holds an archaic position in SLE as a unique classification criterium and pathogenic factor. In a wider sense, antibodies to unique transcriptionally active or silent DNA structures and chromatin components may have individual and profound nephritogenic impact although not considered yet – not in theoretical nor in descriptive or experimental contexts. This hypothesis is contemplated here. In this analysis, our state-of-the-art conception of these antibodies is probed and found too deficient with respect to their origin, structural DNA specificities and clinical/pathogenic impact. Discoveries of DNA structures and functions started with Miescher’s Nuclein (1871), via Chargaff, Franklin, Watson and Crick, and continues today. The discoveries have left us with a DNA helix that presents distinct structures expressing unique operations of DNA. All structures are proven immunogenic! Unique autoimmune antibodies are described against e.g. ssDNA, elongated B DNA, bent B DNA, Z DNA, cruciform DNA, or individual components of chromatin. In light of the massive scientific interest in anti-DNA antibodies over decades, it is an unexpected observation that the spectrum of DNA structures has been known for decades without being implemented in clinical immunology. This leads consequently to a critical analysis of historical and contemporary evidence-based data and of ignored and one-dimensional contexts and hypotheses: i.e. “one antibody - one disease”. In this study radical viewpoints on the impact of DNA and chromatin immunity/autoimmunity are considered and discussed in context of the pathogenesis of lupus nephritis.
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Affiliation(s)
- Ole Petter Rekvig
- Section of Autoimmunity, Fürst Medical Laboratory, Oslo, Norway.,Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
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3
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Protein Expression Level Changes in Weissella koreensis during Garlic Media Fermentation. BIOLOGY 2021; 10:biology10060478. [PMID: 34071410 PMCID: PMC8226471 DOI: 10.3390/biology10060478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 12/05/2022]
Abstract
Simple Summary Garlic is used in cooking and is known to have antibacterial properties due to various organic sulfur components. Weissella koreensis is one of the lactic acid bacteria used for fermentation with garlic and is a strain found in kimchi in Korea, one of foods to which garlic is added. In this study, the addition of garlic to the medium did not cause a difference in growth of W. koreensis. However, the addition of garlic to the growth medium did produce changes in the amount of specific W. koreensis proteins. This study provides basic information about the effect of garlic on fermentation using W. koreensis. Abstract This study investigated the changes in Weissella koreensis (WK) protein expression levels during fermentation in MRS medium supplemented with garlic of WK. WK was first discovered as lactic acid bacteria (LAB) in a Korean fermented cabbage dish known as kimchi. The number of WK cells in MRS medium with garlic (MBCG) and without (MB) after 7 days was 3.55 × 1010 and 2.55 × 1010 CFU/mL, respectively. To observe the changes in the carbon sources in the media, we measured the glucose, sucrose, lactic acid, and acetic acid levels in each medium (MB and MBCG). Thus, 67.2 ± 2.4 (MB) and 64.2 ± 4.7 (MBCG) mmol−1 of glucose were consumed. For sucrose, the level was 3.5 ± 2.2 (MB), and 3.4 ± 2.5 (MBCG) mmol−1. There was not much difference in the lactic acid and acetic acid levels at 160.8 ± 0.4 (MB) and 159.2 ± 0.2 (MBCG) and 2.4 ± 0.4 (MB) and 2.2 ± 8.1 (MBCG) mmol−1, respectively. After the 7-day fermentation period, two-dimensional electrophoresis (2DE) was used to confirm the protein expression pattern in the WK strain. The results show that the fusA and ssb1 proteins were reduced, and the clpP protein was increased. Afterwards, the expression patterns of the above proteins were confirmed through qRT-PCR. Thus, this study confirms the changes in protein expression levels in Weissella koreensis when garlic was added to the media. This study provides basic data for future studies on the major biosynthetic pathways of WK.
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Alswady-Hoff M, Erdem JS, Phuyal S, Knittelfelder O, Sharma A, Fonseca DDM, Skare Ø, Slupphaug G, Zienolddiny S. Long-Term Exposure to Nanosized TiO 2 Triggers Stress Responses and Cell Death Pathways in Pulmonary Epithelial Cells. Int J Mol Sci 2021; 22:ijms22105349. [PMID: 34069552 PMCID: PMC8161419 DOI: 10.3390/ijms22105349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 02/03/2023] Open
Abstract
There is little in vitro data available on long-term effects of TiO2 exposure. Such data are important for improving the understanding of underlying mechanisms of adverse health effects of TiO2. Here, we exposed pulmonary epithelial cells to two doses (0.96 and 1.92 µg/cm2) of TiO2 for 13 weeks and effects on cell cycle and cell death mechanisms, i.e., apoptosis and autophagy were determined after 4, 8 and 13 weeks of exposure. Changes in telomere length, cellular protein levels and lipid classes were also analyzed at 13 weeks of exposure. We observed that the TiO2 exposure increased the fraction of cells in G1-phase and reduced the fraction of cells in G2-phase, which was accompanied by an increase in the fraction of late apoptotic/necrotic cells. This corresponded with an induced expression of key apoptotic proteins i.e., BAD and BAX, and an accumulation of several lipid classes involved in cellular stress and apoptosis. These findings were further supported by quantitative proteome profiling data showing an increase in proteins involved in cell stress and genomic maintenance pathways following TiO2 exposure. Altogether, we suggest that cell stress response and cell death pathways may be important molecular events in long-term health effects of TiO2.
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Affiliation(s)
- Mayes Alswady-Hoff
- National Institute of Occupational Health, NO-0033 Oslo, Norway; (M.A.-H.); (J.S.E.); (S.P.); (Ø.S.)
| | - Johanna Samulin Erdem
- National Institute of Occupational Health, NO-0033 Oslo, Norway; (M.A.-H.); (J.S.E.); (S.P.); (Ø.S.)
| | - Santosh Phuyal
- National Institute of Occupational Health, NO-0033 Oslo, Norway; (M.A.-H.); (J.S.E.); (S.P.); (Ø.S.)
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, NO-0316 Oslo, Norway
| | | | - Animesh Sharma
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway; (A.S.); (D.d.M.F.); (G.S.)
- Proteomics and Metabolomics Core Facility (PROMEC), Norwegian University of Science and Technology and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| | - Davi de Miranda Fonseca
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway; (A.S.); (D.d.M.F.); (G.S.)
- Proteomics and Metabolomics Core Facility (PROMEC), Norwegian University of Science and Technology and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| | - Øivind Skare
- National Institute of Occupational Health, NO-0033 Oslo, Norway; (M.A.-H.); (J.S.E.); (S.P.); (Ø.S.)
| | - Geir Slupphaug
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway; (A.S.); (D.d.M.F.); (G.S.)
- Proteomics and Metabolomics Core Facility (PROMEC), Norwegian University of Science and Technology and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| | - Shanbeh Zienolddiny
- National Institute of Occupational Health, NO-0033 Oslo, Norway; (M.A.-H.); (J.S.E.); (S.P.); (Ø.S.)
- Correspondence: ; Tel.: +47-23195284
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5
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Sharma S, Mukherjee AK, Roy SS, Bagri S, Lier S, Verma M, Sengupta A, Kumar M, Nesse G, Pandey DP, Chowdhury S. Human telomerase is directly regulated by non-telomeric TRF2-G-quadruplex interaction. Cell Rep 2021; 35:109154. [PMID: 34010660 PMCID: PMC7611063 DOI: 10.1016/j.celrep.2021.109154] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/15/2021] [Accepted: 04/28/2021] [Indexed: 12/16/2022] Open
Abstract
Human telomerase reverse transcriptase (hTERT) remains suppressed in most normal somatic cells. Resulting erosion of telomeres leads eventually to replicative senescence. Reactivation of hTERT maintains telomeres and triggers progression of >90% of cancers. However, any direct causal link between telomeres and telomerase regulation remains unclear. Here, we show that the telomere-repeat-binding-factor 2 (TRF2) binds hTERT promoter G-quadruplexes and recruits the polycomb-repressor EZH2/PRC2 complex. This is causal for H3K27 trimethylation at the hTERT promoter and represses hTERT in cancer as well as normal cells. Two highly recurrent hTERT promoter mutations found in many cancers, including ∼83% glioblastoma multiforme, that are known to destabilize hTERT promoter G-quadruplexes, showed loss of TRF2 binding in patient-derived primary glioblastoma multiforme cells. Ligand-induced G-quadruplex stabilization restored TRF2 binding, H3K27-trimethylation, and hTERT re-suppression. These results uncover a mechanism of hTERT regulation through a telomeric factor, implicating telomere-telomerase molecular links important in neoplastic transformation, aging, and regenerative therapy.
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Affiliation(s)
- Shalu Sharma
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Ananda Kishore Mukherjee
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Shuvra Shekhar Roy
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Sulochana Bagri
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Silje Lier
- Department of Microbiology, Oslo University Hospital, Oslo, Norway; Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Meenakshi Verma
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Antara Sengupta
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Manish Kumar
- Imaging Facility, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Gaute Nesse
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | | | - Shantanu Chowdhury
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; GNR Knowledge Centre for Genome and Informatics, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India.
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6
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Carrino S, Hennecker CD, Murrieta AC, Mittermaier A. Frustrated folding of guanine quadruplexes in telomeric DNA. Nucleic Acids Res 2021; 49:3063-3076. [PMID: 33693924 PMCID: PMC8034632 DOI: 10.1093/nar/gkab140] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 01/22/2021] [Accepted: 02/19/2021] [Indexed: 11/23/2022] Open
Abstract
Human chromosomes terminate in long, single-stranded, DNA overhangs of the repetitive sequence (TTAGGG)n. Sets of four adjacent TTAGGG repeats can fold into guanine quadruplexes (GQ), four-stranded structures that are implicated in telomere maintenance and cell immortalization and are targets in cancer therapy. Isolated GQs have been studied in detail, however much less is known about folding in long repeat sequences. Such chains adopt an enormous number of configurations containing various arrangements of GQs and unfolded gaps, leading to a highly frustrated energy landscape. To better understand this phenomenon, we used mutagenesis, thermal melting, and global analysis to determine stability, kinetic, and cooperativity parameters for GQ folding within chains containing 8–12 TTAGGG repeats. We then used these parameters to simulate the folding of 32-repeat chains, more representative of intact telomeres. We found that a combination of folding frustration and negative cooperativity between adjacent GQs increases TTAGGG unfolding by up to 40-fold, providing an abundance of unfolded gaps that are potential binding sites for telomeric proteins. This effect was most pronounced at the chain termini, which could promote telomere extension by telomerase. We conclude that folding frustration is an important and largely overlooked factor controlling the structure of telomeric DNA.
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Affiliation(s)
- Simone Carrino
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
| | - Christopher D Hennecker
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
| | - Ana C Murrieta
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada.,School of Engineering and Sciences, Instituto Tecnológico y de Estudios Superiores De Monterrey, Av. Eugenio Garza Sada 2501 Sur Col. Tecnológico C.P. 64849, Monterrey, Nuevo León, México
| | - Anthony Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
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Hadzic M, Haveric S, Haveric A, Lojo-Kadric N, Galic B, Ramic J, Pojskic L. Bioflavonoids protect cells against halogenated boroxine-induced genotoxic damage by upregulation of hTERT expression. ACTA ACUST UNITED AC 2018; 74:125-129. [DOI: 10.1515/znc-2018-0132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/23/2018] [Indexed: 12/22/2022]
Abstract
Abstract
Plant bioflavonoids are widely present in the human diet and have various protective properties. In this study, we have demonstrated the capacity of delphinidin and luteolin to increase human telomerase reverse transcriptase (hTERT) expression level and act as protective agents against halogenated boroxine-induced genotoxic damage. Halogenated boroxine K2(B3O3F4OH) (HB), is a novel compound with potential for the treatment of both benign and malignant skin changes. In vivo and in vitro studies have confirmed the inhibitory effects of HB on carcinoma cell proliferation and cell cycle progression as well as enzyme inhibition. However, minor genotoxic effects of HB are registered in higher applied concentrations, but those can be suppressed by in vitro addition of delphinidin and luteolin in appropriate concentrations. Fresh peripheral blood samples were cultivated for 72 h followed by independent and concomitant treatments of HB with luteolin or delphinidin. We analyzed the differences in relative hTERT expression between series of treatments compared with controls, which were based on normalized ratios with housekeeping genes. The obtained results have shown that selected bioflavonoids induce upregulation of hTERT that may contribute to the repair of genotoxic damage in vitro.
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Affiliation(s)
- Maida Hadzic
- Institute for Genetic Engineering and Biotechnology , University of Sarajevo , Zmaja od Bosne 8 , 71000 Sarajevo , Bosnia and Herzegovina
| | - Sanin Haveric
- Institute for Genetic Engineering and Biotechnology , University of Sarajevo , Zmaja od Bosne 8 , 71000 Sarajevo , Bosnia and Herzegovina
| | - Anja Haveric
- Institute for Genetic Engineering and Biotechnology , University of Sarajevo , Zmaja od Bosne 8 , 71000 Sarajevo , Bosnia and Herzegovina
| | - Naida Lojo-Kadric
- Institute for Genetic Engineering and Biotechnology , University of Sarajevo , Zmaja od Bosne 8 , 71000 Sarajevo , Bosnia and Herzegovina
| | - Borivoj Galic
- Faculty of Science, Department for Chemistry , University of Sarajevo , Zmaja od Bosne 33-35 , 71000 Sarajevo , Bosnia and Herzegovina
| | - Jasmin Ramic
- Institute for Genetic Engineering and Biotechnology , University of Sarajevo , Zmaja od Bosne 8 , 71000 Sarajevo , Bosnia and Herzegovina
| | - Lejla Pojskic
- Institute for Genetic Engineering and Biotechnology , University of Sarajevo , Zmaja od Bosne 8 , 71000 Sarajevo , Bosnia and Herzegovina
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8
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Gaur P, Hunt CR, Pandita TK. Emerging therapeutic targets in esophageal adenocarcinoma. Oncotarget 2018; 7:48644-48655. [PMID: 27102294 PMCID: PMC5217045 DOI: 10.18632/oncotarget.8777] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/10/2016] [Indexed: 12/18/2022] Open
Abstract
The incidence of gastro-esophageal disease and associated rate of esophageal adenocarcinoma (EAC) is rising at an exponential rate in the United States. However, research targeting EAC is lagging behind, and much research is needed in the field to identify ways to diagnose EAC early as well as to improve the rate of pathologic complete response (pCR) to systemic therapies. Esophagectomy with subsequent reconstruction is known to be a morbid procedure that significantly impacts a patient's quality of life. If indeed the pCR rate of patients can be improved and those patients destined to be pCR can be identified ahead of time, they may be able to avoid this life-altering procedure. While cancer-specific biological pathways have been thoroughly investigated in other solid malignancies, much remains unexplored in EAC. In this review, we will highlight some of the latest research in the field in regards with EAC, along with new therapeutic targets that are currently being explored. After reviewing conventional treatment and current changes in medical therapy for EAC, we will focus on unchartered grounds such as cancer stem cells, genetics and epigenetics, immunotherapy, and chemoradio-resistant pathways as we simultaneously propose some investigational possibilities that could be applicable to EAC.
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Affiliation(s)
- Puja Gaur
- Department of General Surgery, Division of Thoracic Surgery, The Houston Methodist Research Institute, Houston, TX, USA
| | - Clayton R Hunt
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX, USA
| | - Tej K Pandita
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX, USA
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9
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Li Q, Qu F, Li R, He X, Zhai Y, Chen W, Zheng Y. A functional polymorphism of SSBP1 gene predicts prognosis and response to chemotherapy in resected gastric cancer patients. Oncotarget 2017; 8:110861-110876. [PMID: 29340022 PMCID: PMC5762290 DOI: 10.18632/oncotarget.22864] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/03/2017] [Indexed: 12/17/2022] Open
Abstract
Growing evidence has indicated that single-stranded DNA-binding proteins 1 (SSBP1) is involved in tumor initiation and progression. However, effects of single nucleotide polymorphisms (SNPs) in SSBP1 gene on gastric cancer (GC) prognosis are still unknown. In present study, two functional SNPs from SSBP1 were selected and genotyped in a large cohorts of 1030 resected GC patients (326 in the training set, 704 in the validation set) to explore the association of SNPs with patients’ survival. The rs6976500 G allele (CG/GG) genotypes were found significantly associated with both worse overall survival (OS) and recurrence-free survival (RFS) in the training and the independent validation set when compared to C allele genotype, which reaching a more robust statistical significance in the pooled analysis. Furthermore, integration of rs6976500 genotypes and TNM stage significantly improved the prognosis prediction models based on TNM stage alone. In addition, only carriers with at least one G allele of rs6976500 gained significant survival benefit from FOLFOX-based ACT. Mechanistically, SNP rs6976500 G allele genotype could significantly decrease promoter transcriptional activity and markedly reduce expression level of SSBP1 compared with the C allele genotype in GC cells. This was further substantiated by immunohistochemical assay in 70 GC tissue samples. Our study presents the first evidence that SNP rs6976500 G allele genotypes might contribute to GC prognosis by attenuating SSBP1 promoter activity and gene expression, and provides the guidance in refining therapeutic decisions of GC patients. Further exploration on its function is needed to clarify the exact biological mechanism behind.
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Affiliation(s)
- Qiuchen Li
- Department of Gastroenterology, First Affiliated Hospital of the Medical College, Shihezi University, Shihezi, Xinjiang, 832008, China
| | - Falin Qu
- Department of General Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, 710038, China
| | - Renli Li
- Department of General Surgery, The Fourth Hospital of Chinese PLA, Xining, Qinghai, 810007, China
| | - Xianli He
- Department of General Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, 710038, China
| | - Yulong Zhai
- Department of General Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, 710038, China
| | - Weigang Chen
- Department of Gastroenterology, First Affiliated Hospital of the Medical College, Shihezi University, Shihezi, Xinjiang, 832008, China
| | - Yong Zheng
- Department of Gastroenterology, First Affiliated Hospital of the Medical College, Shihezi University, Shihezi, Xinjiang, 832008, China
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10
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Ssb1 and Ssb2 cooperate to regulate mouse hematopoietic stem and progenitor cells by resolving replicative stress. Blood 2017; 129:2479-2492. [PMID: 28270450 DOI: 10.1182/blood-2016-06-725093] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 02/26/2017] [Indexed: 12/14/2022] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) are vulnerable to endogenous damage and defects in DNA repair can limit their function. The 2 single-stranded DNA (ssDNA) binding proteins SSB1 and SSB2 are crucial regulators of the DNA damage response; however, their overlapping roles during normal physiology are incompletely understood. We generated mice in which both Ssb1 and Ssb2 were constitutively or conditionally deleted. Constitutive Ssb1/Ssb2 double knockout (DKO) caused early embryonic lethality, whereas conditional Ssb1/Ssb2 double knockout (cDKO) in adult mice resulted in acute lethality due to bone marrow failure and intestinal atrophy featuring stem and progenitor cell depletion, a phenotype unexpected from the previously reported single knockout models of Ssb1 or Ssb2 Mechanistically, cDKO HSPCs showed altered replication fork dynamics, massive accumulation of DNA damage, genome-wide double-strand breaks enriched at Ssb-binding regions and CpG islands, together with the accumulation of R-loops and cytosolic ssDNA. Transcriptional profiling of cDKO HSPCs revealed the activation of p53 and interferon (IFN) pathways, which enforced cell cycling in quiescent HSPCs, resulting in their apoptotic death. The rapid cell death phenotype was reproducible in in vitro cultured cDKO-hematopoietic stem cells, which were significantly rescued by nucleotide supplementation or after depletion of p53. Collectively, Ssb1 and Ssb2 control crucial aspects of HSPC function, including proliferation and survival in vivo by resolving replicative stress to maintain genomic stability.
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11
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Pandita TK. Critical role of the POT1 OB domain in maintaining genomic stability. Oncogene 2016; 36:1908-1910. [PMID: 27869169 DOI: 10.1038/onc.2016.365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 08/19/2016] [Indexed: 01/14/2023]
Abstract
Oligonucleotide/oligosaccharide-binding (OB) domain-containing proteins have been identified as critical for telomere maintenance, DNA repair, transcription and other DNA metabolism processes. Protection of telomere 1 (POT1), a telomere binding protein, has an OB domain like single-strand binding protein (SSB1). In this issue of Oncogene, Gu et al. present evidence that POT1, like SSB1, is required to maintain genomic stability. This work, in conjunction with results from previous investigators, highlights the importance of POT1 in telomere metabolism. Inactivation of POT1 telomere protective functions in mouse models lacking p53 expression in the breast epithelium unleashes a torrent of DNA damage responses (DDRs) at the telomeres, culminating in karyotypic alterations with massive arrays of telomere fusions. Therefore, POT1 is not only required to promote telomere homeostasis, but also plays an essential role in maintaining a stable genome.
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Affiliation(s)
- T K Pandita
- Department of Radiation Oncology, The Houston Methodist Research Institute, Weill Cornell Medical College, The Houston Methodist Hospital, Houston, TX, USA
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12
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Kariawasam R, Touma C, Cubeddu L, Gamsjaeger R. Backbone (1)H, (13)C and (15)N resonance assignments of the OB domain of the single stranded DNA-binding protein hSSB1 (NABP2/OBFC2B) and chemical shift mapping of the DNA-binding interface. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:297-300. [PMID: 27193589 DOI: 10.1007/s12104-016-9687-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/13/2016] [Indexed: 06/05/2023]
Abstract
Single-stranded DNA-binding proteins (SSBs) are highly important in DNA metabolism and play an essential role in all major DNA repair pathways. SSBs are generally characterised by the presence of an oligonucleotide binding (OB) fold which is able to recognise single-stranded DNA (ssDNA) with high affinity. We discovered two news SSBs in humans (hSSB1 and hSSB2) that both contain a single OB domain followed by a divergent spacer region and a charged C-terminus. We have extensively characterised one of these, hSSB1 (NABP2/OBFC2B), in numerous important DNA processing events such as, in DNA double-stranded break repair and in the response to oxidative DNA damage. Although the structure of hSSB1 bound to ssDNA has recently been determined using X-ray crystallography, the detailed atomic level mechanism of the interaction of hSSB1 with ssDNA in solution has not been established. In this study we report the solution-state backbone chemical shift assignments of the OB domain of hSSB1. In addition, we have utilized NMR to map the DNA-binding interface of hSSB1, revealing major differences between recognition of ssDNA under physiological conditions and in the recently determined crystal structure. Our NMR data in combination with further biophysical and biochemical experiments will allow us to address these discrepancies and shed light onto the structural basis of DNA-binding by hSSB1 in solution.
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Affiliation(s)
- Ruvini Kariawasam
- School of Science and Health, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Christine Touma
- School of Science and Health, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Liza Cubeddu
- School of Science and Health, Western Sydney University, Penrith, NSW, 2751, Australia.
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Roland Gamsjaeger
- School of Science and Health, Western Sydney University, Penrith, NSW, 2751, Australia.
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
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13
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Rienzo M, Casamassimi A. Integrator complex and transcription regulation: Recent findings and pathophysiology. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1859:1269-80. [PMID: 27427483 DOI: 10.1016/j.bbagrm.2016.07.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 07/08/2016] [Accepted: 07/12/2016] [Indexed: 12/20/2022]
Abstract
In the last decade, a novel molecular complex has been added to the RNA polymerase II-mediated transcription machinery as one of the major components. This multiprotein complex, named Integrator, plays a pivotal role in the regulation of most RNA Polymerase II-dependent genes. This complex consists of at least 14 different subunits. However, studies investigating its structure and composition are still lacking. Although it was originally discovered as a complex implicated in the 3'-end formation of noncoding small nuclear RNAs, recent studies indicate additional roles for Integrator in transcription regulation, for example during transcription pause-release and elongation of polymerase, in the biogenesis of transcripts derived from enhancers, as well as in DNA and RNA metabolism for some of its components. Noteworthy, several subunits have been emerging to play roles during development and differentiation; more importantly, their alterations are likely to be involved in several human pathologies, including cancer and lung diseases.
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Affiliation(s)
- Monica Rienzo
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via L. De Crecchio 7, 80138 Naples, Italy
| | - Amelia Casamassimi
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via L. De Crecchio 7, 80138 Naples, Italy.
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14
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Touma C, Kariawasam R, Gimenez AX, Bernardo RE, Ashton NW, Adams MN, Paquet N, Croll TI, O'Byrne KJ, Richard DJ, Cubeddu L, Gamsjaeger R. A structural analysis of DNA binding by hSSB1 (NABP2/OBFC2B) in solution. Nucleic Acids Res 2016; 44:7963-73. [PMID: 27387285 PMCID: PMC5027503 DOI: 10.1093/nar/gkw617] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/28/2016] [Indexed: 02/07/2023] Open
Abstract
Single-stranded DNA binding proteins (SSBs) play an important role in DNA processing events such as replication, recombination and repair. Human single-stranded DNA binding protein 1 (hSSB1/NABP2/OBFC2B) contains a single oligosaccharide/oligonucleotide binding (OB) domain followed by a charged C-terminus and is structurally homologous to the SSB from the hyperthermophilic crenarchaeote Sulfolobus solfataricus. Recent work has revealed that hSSB1 is critical to homologous recombination and numerous other important biological processes such as the regulation of telomeres, the maintenance of DNA replication forks and oxidative damage repair. Since the ability of hSSB1 to directly interact with single-stranded DNA (ssDNA) is paramount for all of these processes, understanding the molecular details of ssDNA recognition is essential. In this study, we have used solution-state nuclear magnetic resonance in combination with biophysical and functional experiments to structurally analyse ssDNA binding by hSSB1. We reveal that ssDNA recognition in solution is modulated by base-stacking of four key aromatic residues within the OB domain. This DNA binding mode differs significantly from the recently determined crystal structure of the SOSS1 complex containing hSSB1 and ssDNA. Our findings elucidate the detailed molecular mechanism in solution of ssDNA binding by hSSB1, a major player in the maintenance of genomic stability.
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Affiliation(s)
- Christine Touma
- School of Science and Health, Western Sydney University, Penrith, NSW 2751, Australia
| | - Ruvini Kariawasam
- School of Science and Health, Western Sydney University, Penrith, NSW 2751, Australia
| | - Adrian X Gimenez
- School of Science and Health, Western Sydney University, Penrith, NSW 2751, Australia
| | - Ray E Bernardo
- School of Science and Health, Western Sydney University, Penrith, NSW 2751, Australia
| | - Nicholas W Ashton
- School of Biomedical Research, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD 4102, Australia
| | - Mark N Adams
- School of Biomedical Research, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD 4102, Australia
| | - Nicolas Paquet
- School of Biomedical Research, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD 4102, Australia
| | - Tristan I Croll
- School of Biomedical Research, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD 4102, Australia
| | - Kenneth J O'Byrne
- School of Biomedical Research, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD 4102, Australia
| | - Derek J Richard
- School of Biomedical Research, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD 4102, Australia
| | - Liza Cubeddu
- School of Science and Health, Western Sydney University, Penrith, NSW 2751, Australia School of Molecular Biosciences, University of Sydney, NSW 2006, Australia
| | - Roland Gamsjaeger
- School of Science and Health, Western Sydney University, Penrith, NSW 2751, Australia School of Molecular Biosciences, University of Sydney, NSW 2006, Australia
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15
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Azhibek D, Skvortsov D, Andreeva A, Zatsepin T, Arutyunyan A, Zvereva M, Dontsova O. TERRA mimicking ssRNAs prevail over the DNA substrate for telomerase in vitro due to interactions with the alternative binding site. J Mol Recognit 2015; 29:242-7. [PMID: 26669798 DOI: 10.1002/jmr.2521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 10/23/2015] [Accepted: 10/24/2015] [Indexed: 12/12/2022]
Abstract
Telomerase is a key component of the telomere length maintenance system in the majority of eukaryotes. Telomerase displays maximal activity in stem and cancer cells with high proliferative potential. In humans, telomerase activity is regulated by various mechanisms, including the interaction with telomere ssDNA overhangs that contain a repetitive G-rich sequence, and with noncoding RNA, Telomeric repeat-containing RNA (TERRA), that contains the same sequence. So these nucleic acids can compete for telomerase RNA templates in the cell. In this study, we have investigated the ability of different model substrates mimicking telomere DNA overhangs and TERRA RNA to compete for telomerase in vitro through a previously developed telomerase inhibitor assay. We have shown in this study that RNA oligonucleotides are better competitors for telomerase that DNA ones as RNA also use an alternative binding site on telomerase, and the presence of 2'-OH groups is significant in these interactions. In contrast to DNA, the possibility of forming intramolecular G-quadruplex structures has a minor effect for RNA binding to telomerase. Taking together our data, we propose that TERRA RNA binds better to telomerase compared with its native substrate - the 3'-end of telomere DNA overhang. As a result, some specific factor may exist that participates in switching telomerase from TERRA to the 3'-end of DNA for telomere elongation at the distinct period of a cell cycle in vivo. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- Dulat Azhibek
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,Skolkovo Institute of Science and Technology, 4 Alfred Nobel Street, Skolkovo, 143025, Russia
| | - Dmitry Skvortsov
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Anna Andreeva
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Timofei Zatsepin
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,Skolkovo Institute of Science and Technology, 4 Alfred Nobel Street, Skolkovo, 143025, Russia
| | - Alexandr Arutyunyan
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Maria Zvereva
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Olga Dontsova
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
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16
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Chakraborty A, Wakamiya M, Venkova-Canova T, Pandita RK, Aguilera-Aguirre L, Sarker AH, Singh DK, Hosoki K, Wood TG, Sharma G, Cardenas V, Sarkar PS, Sur S, Pandita TK, Boldogh I, Hazra TK. Neil2-null Mice Accumulate Oxidized DNA Bases in the Transcriptionally Active Sequences of the Genome and Are Susceptible to Innate Inflammation. J Biol Chem 2015; 290:24636-48. [PMID: 26245904 PMCID: PMC4598976 DOI: 10.1074/jbc.m115.658146] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 07/27/2015] [Indexed: 12/11/2022] Open
Abstract
Why mammalian cells possess multiple DNA glycosylases (DGs) with overlapping substrate ranges for repairing oxidatively damaged bases via the base excision repair (BER) pathway is a long-standing question. To determine the biological role of these DGs, null animal models have been generated. Here, we report the generation and characterization of mice lacking Neil2 (Nei-like 2). As in mice deficient in each of the other four oxidized base-specific DGs (OGG1, NTH1, NEIL1, and NEIL3), Neil2-null mice show no overt phenotype. However, middle-aged to old Neil2-null mice show the accumulation of oxidative genomic damage, mostly in the transcribed regions. Immuno-pulldown analysis from wild-type (WT) mouse tissue showed the association of NEIL2 with RNA polymerase II, along with Cockayne syndrome group B protein, TFIIH, and other BER proteins. Chromatin immunoprecipitation analysis from mouse tissue showed co-occupancy of NEIL2 and RNA polymerase II only on the transcribed genes, consistent with our earlier in vitro findings on NEIL2's role in transcription-coupled BER. This study provides the first in vivo evidence of genomic region-specific repair in mammals. Furthermore, telomere loss and genomic instability were observed at a higher frequency in embryonic fibroblasts from Neil2-null mice than from the WT. Moreover, Neil2-null mice are much more responsive to inflammatory agents than WT mice. Taken together, our results underscore the importance of NEIL2 in protecting mammals from the development of various pathologies that are linked to genomic instability and/or inflammation. NEIL2 is thus likely to play an important role in long term genomic maintenance, particularly in long-lived mammals such as humans.
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Affiliation(s)
- Anirban Chakraborty
- From the Department of Internal Medicine, Sealy Center for Molecular Medicine
| | - Maki Wakamiya
- Departments of Neurology and Neuroscience and Cell Biology, Transgenic Mouse Core Facility, University of Texas Medical Branch, Galveston, Texas 77555
| | | | - Raj K Pandita
- the Department of Radiation Oncology, Houston Methodist Research Institute, Houston, Texas 77030, and
| | | | - Altaf H Sarker
- the Department of Cancer and DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Dharmendra Kumar Singh
- the Department of Radiation Oncology, Houston Methodist Research Institute, Houston, Texas 77030, and
| | - Koa Hosoki
- From the Department of Internal Medicine, Sealy Center for Molecular Medicine
| | | | - Gulshan Sharma
- From the Department of Internal Medicine, Sealy Center for Molecular Medicine
| | - Victor Cardenas
- From the Department of Internal Medicine, Sealy Center for Molecular Medicine
| | | | - Sanjiv Sur
- From the Department of Internal Medicine, Sealy Center for Molecular Medicine
| | - Tej K Pandita
- the Department of Radiation Oncology, Houston Methodist Research Institute, Houston, Texas 77030, and
| | | | - Tapas K Hazra
- From the Department of Internal Medicine, Sealy Center for Molecular Medicine,
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